grouper: Find groups of correlating samples
In LieberInstitute/brainstorm_package: Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation
Description
Usage
Arguments
Value
Examples
Description
Create groups of sample from a cor table with correlation >= cutoff
Usage
1
grouper(corTable, cutoff = 0.59, s1 = "row_sample", s2 = "col_sample")
Arguments
corTable
Table of paiwise correlation between samples
cutoff
corrlation threshold for samples to be grouped together
s1
Name of first column that contains sample names
s2
Name of second column that contains sample names
Value
List of groups found in the cor table
Examples
1
2
3
4
5
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8
cor_test <- make_corLong(snps1 = test_snps, BrainTable1 = test_BrTable, ID_col1 = "Sample")
g <- grouper(cor_test)
snpsCalled_filter <- filter_called(snpsCalled_VCF)
snpsRNA <- make_snpsRNA(snpsGeno_VCF, snpsCalled_filter)
pd_simple <- pd_example[,1:4]
corLong_rna <- make_corLong(snpsRNA$snpsCalled, BrainTable1 = pd_simple, ID_col1 = "SAMPLE_ID")
groups_rna <- grouper(corLong_rna)
LieberInstitute/brainstorm_package documentation built on Dec. 17, 2021, 12:04 a.m.
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Description Usage Arguments Value Examples
Description
Create groups of sample from a cor table with correlation >= cutoff
Usage
1 | grouper(corTable, cutoff = 0.59, s1 = "row_sample", s2 = "col_sample")
|
Arguments
corTable |
Table of paiwise correlation between samples |
cutoff |
corrlation threshold for samples to be grouped together |
s1 |
Name of first column that contains sample names |
s2 |
Name of second column that contains sample names |
Value
List of groups found in the cor table
Examples
1 2 3 4 5 6 7 8 | cor_test <- make_corLong(snps1 = test_snps, BrainTable1 = test_BrTable, ID_col1 = "Sample")
g <- grouper(cor_test)
snpsCalled_filter <- filter_called(snpsCalled_VCF)
snpsRNA <- make_snpsRNA(snpsGeno_VCF, snpsCalled_filter)
pd_simple <- pd_example[,1:4]
corLong_rna <- make_corLong(snpsRNA$snpsCalled, BrainTable1 = pd_simple, ID_col1 = "SAMPLE_ID")
groups_rna <- grouper(corLong_rna)
|
R Package Documentation
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